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- EMDB-9674: Cryo-EM structure of CV-A10 mature virion -

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Basic information

Entry
Database: EMDB / ID: 9674
TitleCryo-EM structure of CV-A10 mature virion
Map data
SampleCoxsackievirus A10:
virus / VP1 / VP2 / VP3 / VP4 / ligand
Function / homologyPicornavirus capsid / Picornavirus coat protein VP4 / Viral coat protein subunit / Picornavirus/Calicivirus coat protein / picornavirus capsid protein / Picornavirus coat protein (VP4) / viral capsid / structural molecule activity / p1 polyprotein
Function and homology information
SourceCoxsackievirus A10
Methodsingle particle reconstruction / cryo EM / 2.84 Å resolution
AuthorsChen JH / Ye XH / Cong Y / Huang Z
CitationJournal: To Be Published
Title: Structure of CVA10 mature virion
Authors: Chen JH / Ye XH / Cong Y / Huang Z
Validation ReportPDB-ID: 6iij

SummaryFull reportAbout validation report
DateDeposition: Oct 6, 2018 / Header (metadata) release: Nov 7, 2018 / Map release: Nov 7, 2018 / Last update: Nov 7, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6iij
  • Surface level: 1.6
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6iij
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9674.map.gz (map file in CCP4 format, 322487 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
432 pix
1.01 Å/pix.
= 434.16 Å
432 pix
1.01 Å/pix.
= 434.16 Å
432 pix
1.01 Å/pix.
= 434.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.005 Å
Density
Contour Level:1.6 (by author), 1.6 (movie #1):
Minimum - Maximum-9.277205 - 15.515470000000001
Average (Standard dev.)-0.000000000384173 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions432432432
Origin0.00.00.0
Limit431.0431.0431.0
Spacing432432432
CellA=B=C: 434.16 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0051.0051.005
M x/y/z432432432
origin x/y/z0.0000.0000.000
length x/y/z434.160434.160434.160
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS432432432
D min/max/mean-9.27715.515-0.000

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Supplemental data

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Sample components

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Entire Coxsackievirus A10

EntireName: Coxsackievirus A10 / Number of components: 6

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Component #1: virus, Coxsackievirus A10

VirusName: Coxsackievirus A10 / Class: VIRION / Empty: No / Enveloped: No / Isolate: STRAIN
SpeciesSpecies: Coxsackievirus A10

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.088219 kDa
SourceSpecies: Coxsackievirus A10

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Component #3: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.741023 kDa
SourceSpecies: Coxsackievirus A10

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Component #4: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.187623 kDa
SourceSpecies: Coxsackievirus A10

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Component #5: protein, VP4

ProteinName: VP4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.464104 kDa
SourceSpecies: Coxsackievirus A10

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Component #6: ligand, SPHINGOSINE

LigandName: SPHINGOSINE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.299492 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 8 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 13273
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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